lmsba(1)

💖 lmsba(1) 💖

okay so bestie, pull up a chair 🫶 this page is all about lmsba, and it lives inside The Computational Morphology Toolkit — CMTK, iykyk 😌 and before you come for me: yes, that is literally the full toolkit name, I did not make it up for drama 💅

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🌸 NAME 🌸

lmsba — Local voting. that's it. that's the whole name. short, iconic, main character energy ✨

✨ SYNOPSIS ✨

lsba [options] targetImage atlasIntensity1 atlasLabels1 [atlasIntensity2
atlasLabels2 [...]]

(and yes, it says lsba in there — exactly like that, I'm just reading it to you fr fr 🙈)

💅 DESCRIPTION 💅

so what does this thing actually DO. picture this: you've got a whole little group chat of multi-class segmentations, all of them coming from atlases that are already co-registered and reformatted. lmsba combines all of them together using locally-weighted Shape-Based Averaging 🦋

many atlas opinions in, one combined result out. it's giving collaborative. it's giving consensus. it ate 👑

🎀 OPTIONS 🎀

🌈 Global Toolkit Options (these are shared by all CMTK tools) 🌈

• --help — writes the list of basic command line options to standard output. baby's first --help, we love to see it 💖
• --help-all — writes the complete list of basic and advanced command line options to standard output. the full lore drop 😭
• --wiki — writes the list of command line options to standard output in MediaWiki markup. for when your docs live on a wiki bestie 🎀
• --man — writes man page source in 'nroff' markup to standard output. meta. we're in a manpage and it can print manpages 🌈
• --version — writes toolkit version to standard output. vibe check the version, always ✨
• --echo — writes the current command line to standard output. so you can see exactly what you just ran 👀
• --verbose-level <integer> — set verbosity level. dial the yapping up or down 🔥
• --verbose, -v — increment verbosity level by 1. heads up though: this one is deprecated; it's only supported for backward compatibility 🫶
• --threads <integer> — set maximum number of parallel threads (for POSIX threads and OpenMP). make it go brrr 💅

🫶 Input Options 🫶

• --set-padding-value <double> — set the padding value for input intensity images. pixels that have this value get ignored, so they don't mess with your results. [Default: disabled] 🚫

🦋 Label Combination Options 🦋

• --patch-radius <none> — the radius of the image patch (in pixels) used for local similarity computation. [Default: 5]
• --search-radius <none> — the search radius for local image patch matching. the algorithm goes out and finds the best-matching patch within this radius by exhaustive search — like, it checks everything, no shortcuts 😤 [Default: 0]
• --no-local-outliers — detect and exclude local outliers in the Shape Based Averaging procedure. bye felicia 👋
• --no-global-outliers — detect and exclude global outliers by removing poorly correlated atlases before the local SBA procedure even starts. preemptive blocking, iconic 💀

⭐ Output Options ⭐

• --output <string>, -o <string> — the file system path for the output image. tell it where to drop your masterpiece. [Default: lsbo.nii ]

👑 AUTHORS 👑

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko 💜

📜 LICENSE 📜

http://www.fsf.org/licensing/licenses/gpl.html

🐛 BUGS 🐛

found a bug? report it at http://nitrc.org/projects/cmtk/ — the devs wanna know, fr fr 🙈

🎀 ACKNOWLEDGMENTS 🎀

CMTK is developed with support from the NIAAA under Grant AA021697, National Consortium on Alcohol and Neurodevelopment in Adolescence (N-CANDA): Data Integration Component. And from April 2009 through September 2011, CMTK development and maintenance was supported by the NIBIB under Grant EB008381. funding besties, we appreciate you 🫶🌈

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and that's the whole page, bestie — this one is from CMTK 3.3.1p2, dated Jun 24 2026, and it's the lmsba(1) manual. go forth and average some shapes 💅✨🌸